rs4958846

Variant names:

• chr5-150845576-T-C
• rs4958846

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.252 in 152,102 control chromosomes in the GnomAD database, including 6,981 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (6981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38241 AN: 151986 Hom.: 6961 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.253

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.252 AC: 38300 AN: 152102 Hom.: 6981 Cov.: 32 AF XY: 0.253 AC XY: 18808 AN XY: 74356

African (AFR) AF: 0.478 AC: 19830 AN: 41478

American (AMR) AF: 0.186 AC: 2844 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3157 AN: 5134

South Asian (SAS) AF: 0.273 AC: 1318 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10606

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8464 AN: 67976

Other (OTH) AF: 0.253 AC: 534 AN: 2108

Alfa AF: 0.187 Hom.: 495

Bravo AF: 0.270

Asia WGS AF: 0.416 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.071
PhyloP100		-1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4958846; hg19: chr5-150225138;